Displaying 1 to 3 from 3 results

metacoder - Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

  •    R

The function that simulates PCR requires primersearch from the EMBOSS tool kit to be installed. This is not an R package, so it is not automatically installed. Type ?primersearch after installing and loading metacoder for installation instructions. Many of these operations can be done using other packages like phyloseq, which also provides tools for diversity analysis. The main strength of metacoder is that its functions use the flexible data types defined by taxa, which has powerful parsing and subsetting abilities that take into account the hierarchical relationship between taxa and user-defined data. In general, metacoder and taxa are more of an abstracted tool kit, whereas phyloseq has more specialized functions for community diversity data, but they both can do similar things. I encourage you to try both to see which fits your needs and style best. You can also combine the two in a single analysis by converting between the two data types when needed.

dada2 - Accurate sample inference from amplicon data with single nucleotide resolution

  •    R

Exact sample inference from high-throughput amplicon data. Resolves real variants differing by as little as one nucleotide. Visit the DADA2 website for the most detailed and up-to-date documentation. In order to install dada2 from source (and get the latest and greatest new features) see our installation from source instructions.

decontam - Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

  •    R

An introductory vignette demonstrating how to use the decontam package to identify contaminants. The preprint introducing decontam with benchmarking demonstrating how decontam-inating your data removes reagent sequences, improves accuracy, reduces batch effects, and prevents false-positive assocations.